I have recently brewed an APA. I pitched with White Labs Pacific Ale yeast. I brewed this batch on 8.24.08. After 3 weeks of continual fermentation (air lock bubbling away), I couldn't take it any longer. This is the longest that I have ever seen my fermentation take. So I racked it into a secondary to see if I could "break" the fermentation. I took a FG reading of 1.012, right where I wanted to be. Well, no luck in breaking the fermentation. This morning I have a new Krausen and it is bubbling away, granted, not as vigorous as before. Any ideas as to why this fermentation wont stop??

I fear an infection, as the sample I took for my FG reading had a slight (very slight) vinegar smell and taste.

I had a beer like that. It took 5 weeks to ferment. I never found why. It was a Strong scotch all. OG was 1.1 and FG was 1.14. It finished lot lower than expected. I was also afraid but After a year now, a the beer still taste great...

It's possible it's infected, but I don't think there's any way to know for sure at this point. The flavor issue you mention could be green beer or the result of prematurely terminating the ferment before the yeast had a chance to clean-up after itself, as easily as from an infection.

It's never a good idea to try to stop an active fermentation. You increase your odds of having off flavors and risk bottle bombs, if you bottle.